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- EMDB-54094: Cryo-EM structure of the human potassium chloride cotransporter T... -

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Basic information

Entry
Database: EMDB / ID: EMD-54094
TitleCryo-EM structure of the human potassium chloride cotransporter T906A/T1007A phospho-knockout mutants KCC2b bound ATP in LMNG (outward-facing state, dimer)
Map data
Sample
  • Complex: Dimer structure of KCC2
    • Protein or peptide: Isoform 2 of Solute carrier family 12 member 5
  • Ligand: N-cyclopropyl-N-(4-methyl-1,3-thiazol-2-yl)-2-[(6-phenylpyridazin-3-yl)sulfanyl]acetamide
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: CHLORIDE ION
  • Ligand: SODIUM ION
  • Ligand: water
KeywordsMembrane protein / Transporter / Cation/chloride cotransporter
Function / homology
Function and homology information


thermosensory behavior / intracellular pH reduction / potassium:chloride symporter activity / hypotonic response / Cation-coupled Chloride cotransporters / intracellular chloride ion homeostasis / ammonium channel activity / chloride ion homeostasis / dendritic spine development / postsynaptic neurotransmitter receptor diffusion trapping ...thermosensory behavior / intracellular pH reduction / potassium:chloride symporter activity / hypotonic response / Cation-coupled Chloride cotransporters / intracellular chloride ion homeostasis / ammonium channel activity / chloride ion homeostasis / dendritic spine development / postsynaptic neurotransmitter receptor diffusion trapping / potassium ion homeostasis / cell volume homeostasis / chloride transmembrane transporter activity / postsynaptic specialization membrane / potassium ion import across plasma membrane / regulation of postsynapse assembly / monoatomic ion transport / dendrite membrane / chloride transmembrane transport / cell periphery / learning / multicellular organism growth / chemical synaptic transmission / perikaryon / neuron projection / response to xenobiotic stimulus / neuronal cell body / protein kinase binding / glutamatergic synapse / membrane / metal ion binding / plasma membrane
Similarity search - Function
K/Cl co-transporter / SLC12A transporter, C-terminal / Solute carrier family 12 / SLC12A transporter family / Amino acid permease/ SLC12A domain / Amino acid permease
Similarity search - Domain/homology
Solute carrier family 12 member 5
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.86 Å
AuthorsMatsuoka R / Oswald C / Jazayeri A / Duerr KL
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Distinct cytoplasmic domain interactions control autoinhibition of the neuronal potassium coupled chloride transporter KCC2
Authors: Matsuoka R / Oswald C / Jazayeri A / Duerr KL
History
DepositionJun 19, 2025-
Header (metadata) releaseJul 8, 2026-
Map releaseJul 8, 2026-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54094.png

Downloads & links

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Map

FileReleased
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 300 pix.
= 300.96 Å		1 Å/pix.
x 300 pix.
= 300.96 Å		1 Å/pix.
x 300 pix.
= 300.96 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0032 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.111
Minimum - Maximum-0.16518596 - 0.34590012
Average (Standard dev.)-0.0008923642 (±0.012285989)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 300.96002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54094_msk_1.map
Projections & Slices
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Additional map: #1

Fileemd_54094_additional_1.map
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Half map: #2

Fileemd_54094_half_map_1.map
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Half map: #1

Fileemd_54094_half_map_2.map
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Sample components

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Entire : Dimer structure of KCC2

EntireName: Dimer structure of KCC2
Components
  • Complex: Dimer structure of KCC2
    • Protein or peptide: Isoform 2 of Solute carrier family 12 member 5
  • Ligand: N-cyclopropyl-N-(4-methyl-1,3-thiazol-2-yl)-2-[(6-phenylpyridazin-3-yl)sulfanyl]acetamide
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: CHLORIDE ION
  • Ligand: SODIUM ION
  • Ligand: water

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Supramolecule #1: Dimer structure of KCC2

SupramoleculeName: Dimer structure of KCC2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Isoform 2 of Solute carrier family 12 member 5

MacromoleculeName: Isoform 2 of Solute carrier family 12 member 5 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 129.059773 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGSAWSHPQF EKGGGSGGGS GGSAWSHPQF EKHHHHHHHH HHLEVLFQGP LNNLTDCEDG DGGANPGDGN PKESSPFINS TDTEKGKEY DGKNMALFEE EMDTSPMVSS LLSGLANYTN LPQGSREHEE AENNEGAGKK KPVQAPRMGT FMGVYLPCLQ N IFGVILFL ...String:
MGSAWSHPQF EKGGGSGGGS GGSAWSHPQF EKHHHHHHHH HHLEVLFQGP LNNLTDCEDG DGGANPGDGN PKESSPFINS TDTEKGKEY DGKNMALFEE EMDTSPMVSS LLSGLANYTN LPQGSREHEE AENNEGAGKK KPVQAPRMGT FMGVYLPCLQ N IFGVILFL RLTWVVGIAG IMESFCMVFI CCSCTMLTAI SMSAIATNGV VPAGGSYYMI SRSLGPEFGG AVGLCFYLGT TF AGAMYIL GTIEILLAYL FPAMAIFKAE DASGEAAAML NNMRVYGTCV LTCMATVVFV GVKYVNKFAL VFLGCVILSI LAI YAGVIK SAFDPPNFPI CLLGNRTLSR HGFDVCAKLA WEGNETVTTR LWGLFCSSRF LNATCDEYFT RNNVTEIQGI PGAA SGLIK ENLWSSYLTK GVIVERSGMT SVGLADGTPI DMDHPYVFSD MTSYFTLLVG IYFPSVTGIM AGSNRSGDLR DAQKS IPTG TILAIATTSA VYISSVVLFG ACIEGVVLRD KFGEAVNGNL VVGTLAWPSP WVIVIGSFFS TCGAGLQSLT GAPRLL QAI SRDGIVPFLQ VFGHGKANGE PTWALLLTAC ICEIGILIAS LDEVAPILSM FFLMCYMFVN LACAVQTLLR TPNWRPR FR YYHWTLSFLG MSLCLALMFI CSWYYALVAM LIAGLIYKYI EYRGAEKEWG DGIRGLSLSA ARYALLRLEE GPPHTKNW R PQLLVLVRVD QDQNVVHPQL LSLTSQLKAG KGLTIVGSVL EGTFLENHPQ AQRAEESIRR LMEAEKVKGF CQVVISSNL RDGVSHLIQS GGLGGLQHNT VLVGWPRNWR QKEDHQTWRN FIELVRETTA GHLALLVTKN VSMFPGNPER FSEGSIDVWW IVHDGGMLM LLPFLLRHHK VWRKCKMRIF TVAQMDDNSI QMKKDLTTFL YHLRITAEVE VVEMHESDIS AYTYEKTLVM E QRSQILKQ MHLTKNERER EIQSITDESR GSIRRKNPAN TRLRLNVPEE TAGDSEEKPE EEVQLIHDQS APSCPSSSPS PG EEPEGEG ETDPEKVHLT WTKDKSVAEK NKGPSPVSSE GIKDFFSMKP EWENLNQSNV RRMHTAVRLN EVIVKKSRDA KLV LLNMPG PPRNRNGDEN YMEFLEVLTE HLDRVMLVRG GGREVITIYS

UniProtKB: Solute carrier family 12 member 5

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Macromolecule #2: N-cyclopropyl-N-(4-methyl-1,3-thiazol-2-yl)-2-[(6-phenylpyridazin...

MacromoleculeName: N-cyclopropyl-N-(4-methyl-1,3-thiazol-2-yl)-2-[(6-phenylpyridazin-3-yl)sulfanyl]acetamide
type: ligand / ID: 2 / Number of copies: 2 / Formula: JUX
Molecular weightTheoretical: 382.502 Da
Chemical component information

ChemComp-JUX:
N-cyclopropyl-N-(4-methyl-1,3-thiazol-2-yl)-2-[(6-phenylpyridazin-3-yl)sulfanyl]acetamide

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Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #4: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Macromolecule #5: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 5 / Number of copies: 4
Molecular weightTheoretical: 22.99 Da

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 2 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration3 mg/mL
BufferpH: 6.8
Component:
ConcentrationFormulaName
20.0 mMTris-HClTris
100.0 mMNaClsodium chloride
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 269 K

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 5002 / Average exposure time: 2.0 sec. / Average electron dose: 42.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.86 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 44814
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

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